No I mean put every vehicle's NPC in a seperate .npc file.
If you open the kyle.npc file using notepad or whatever you use for your npcs (can be that very useful NPCTool too), you'll notice that in kyle.npc there is kyle, and kyle_boss. In your case, you would put kyle_boss in it's own file, so now you have kyle.npc and kyle_boss.npc
Hope this all made sense to you, cuz I had trouble explaining it. Hope you can get it to work.